@ncbijs/http-mcp
MCP server exposing NCBI biomedical tools for LLM agents
Versions
0.1.1latest0.0.0Tools 40
drug-lookup Look up a drug in RxNorm by name. Uses fuzzy matching to find the best candidates even with
lookup-variant Retrieve SNP variant data from NCBI dbSNP (Variation Services API). Returns alleles,
search-pubmed Search PubMed for biomedical literature articles. Returns structured metadata
search-related Find PubMed articles related to a given article, ranked by relevancy score.
get-references Get the list of articles referenced by a given PubMed article.
get-cited-by Get the list of articles that cite a given PubMed article.
citation-metrics Get NIH iCite citation metrics for one or more PubMed articles. Returns Relative Citation Ratio (RCR),
citation-graph Get the full citation graph for a PubMed article — all articles that cite it (cited-by)
blast-search Run a BLAST sequence alignment search against NCBI databases. Submits the query,
search-compound Look up a chemical compound in PubChem by name or CID. Returns molecular properties
search-gene-by-compound Find NCBI Gene IDs linked to a PubChem compound by CID.
search-clinvar Search NCBI ClinVar for clinical variants by gene name, variant description,
lookup-refsnp Look up a RefSNP variant by rsID using the NCBI Variation Services API.
lookup-frequency Look up allele frequency data (ALFA) for a variant by rsID.
get-full-text Fetch the full text of a PubMed Central article and return it as markdown.
get-full-text-chunks Fetch a PubMed Central article and split it into semantic chunks suitable for
find-entity Search for biomedical entities (genes, diseases, chemicals, variants, species, cell lines)
annotate-text Annotate free text with biomedical named entity recognition via PubTator3.
export-annotations Export BioC annotations for PubMed articles via PubTator3. Returns structured
search-litvar Search LitVar2 for genetic variants matching a query and find associated literature.
convert-ids Convert between PubMed IDs (PMID), PubMed Central IDs (PMCID), DOIs, and Manuscript IDs (MID).
get-citation Get a formatted citation for a PubMed article. Supports CSL-JSON (structured metadata),
mesh-lookup Look up a Medical Subject Headings (MeSH) descriptor by name or ID via the NLM API.
mesh-sparql Execute a SPARQL query against the NLM MeSH vocabulary. Useful for advanced vocabulary
search-gene Retrieve gene metadata from NCBI Datasets API v2. Search by gene IDs (numeric) or by
lookup-taxonomy Retrieve taxonomy data from NCBI Datasets API v2. Returns organism name, rank,
search-genome Retrieve genome assembly reports from NCBI Datasets API v2. Search by assembly
store-lookup-variant Look up a ClinVar variant by UID from the local store.
store-search-variants Search ClinVar variants in the local store by clinical significance,
store-lookup-gene Look up a gene by NCBI Gene ID from the local store.
store-search-genes Search genes in the local store by symbol, description, type, or tax ID.
store-lookup-mesh Look up a MeSH descriptor by its unique ID (e.g., D000001) from the local store.
store-search-mesh Search MeSH descriptors by name in the local store. Supports exact match,
store-lookup-compound Look up a PubChem compound by CID from the local store.
store-search-compounds Search PubChem compounds in the local store by InChI key, IUPAC name, or SMILES.
store-stats Get record counts and storage statistics for all datasets in the local store.
store-lookup-taxonomy Look up a taxonomy node by tax ID from the local store.
store-search-taxonomy Search taxonomy nodes in the local store by organism name, common name, or rank.
store-convert-ids Convert between PMID, PMCID, DOI, and Manuscript ID using the local store.
store-search-ids Search ID mappings in the local store by PMID, PMCID, DOI, or Manuscript ID field.
Permissions 3
network medium shell high env_vars low Scan Findings 0
No scan findings.